The hepatocyte nuclear factor 4-alpha (HNF4) is a member of the nuclear receptor family of transcription factors. HNF4 controls genes in the liver and pancreas related to insulin and glucose production. Mutations in HNF4 cause Maturity Onset of Diabetes in Young 1 (MODY1), and hyperinsulinemic hypoglycemia (HH) in humans. Members of the nuclear receptor superfamily have a hydrophobic pocket inside their ligand binding domains (LBDs). Traditional drug screening strategies exploit these pockets, guided by known structures of isolated LBDs. The field has lacked high-resolution structures for full-length receptors, and therefore not considered the possibility of other druggable sites elsewhere in these proteins. We have obtained a complete crystal structure HNF4 homodimer, in a functionally revealing complex with its DNA response element. This structure unexpectedly reveals two sites at domain-domain junctions, where small molecules could bind. Our mutational studies, and previous knowledge of post-translational modifications, show these sites can allosterically regulate the DNA affinity of HNF4 . We propose a high-throughput screening campaign, together with confirmatory assays and mechanistic studies that exploit these new sites in HNF4 . Our goal is to identify potentiators of DNA binding that benefit certain MODY1 and HH disease populations where receptor-DNA binding is compromised by point mutations in HNF4 .